Hi,
I'd like to arrive at a set of 2D images (e.g. 'unraveled' myelin maps
obtained by cutting and stretching out the sphere), with anatomical
correspondence across subjects, which can be used as inputs to external
proprietary algorithms (e.g. classification), so I'm pretty sure I'll
need to step out of the Workbench.
Thanks!
Nicola
On 03/29/2017 04:18 PM, Glasser, Matthew wrote:
What operations beyond smoothing do you need? There is wb_command
-cifti-smoothing.
Peace,
Matt.
From: Nicola Toschi <[email protected]
<mailto:[email protected]>>
Date: Wednesday, March 29, 2017 at 9:09 AM
To: Matt Glasser <[email protected] <mailto:[email protected]>>,
"[email protected] <mailto:[email protected]>"
<[email protected] <mailto:[email protected]>>
Subject: Re: [HCP-Users] Position of vertices in myelin maps and 164k
sphere
Hi Matt,
thank you for your quick answer! That makes sense.
I would like to do some spatial operations on the sphere that exploit
spatial neighborhood information (e.g. even simple smoothing or
filtering on the 2D surface), and have these operations be consistent
across subjects.
What would be the best way to go about this do you think? Incorporate
the exact vertex locations for each subject anyway, or ignore them and
(somehow) just use the fact that vertex /n /has the same
neuroanatomical meaning in every subject?
Thanks again,
Nicola
On 03/29/2017 04:02 PM, Glasser, Matthew wrote:
We don¹t recommend using the ft_ tools with MRI data. Instead use
ciftiopen/ciftisave/ciftisavereset:
https://wiki.humanconnectome.org/display/PublicData/HCP+Users+FAQ item 2B
As for your other question, the vertex indices have neuroanatomical
correspondence across subjects, but that often does not equate to having
the same 3D coordinates (as volumetric registration is not able to align
cortical areas across subjects).
Peace,
Matt.
On 3/29/17, 8:41 AM,"[email protected] on behalf of Nicola Toschi" <[email protected] on behalf of
[email protected]> wrote:
Dear List,
I am trying to do some postprocessing on myelin and thickness maps (164k
versions) contained in the MNINonLinear Directory of the Structural
dataset (e.g. ${subject}.corrThickness_MSMAll.164k_fs_LR.dscalar.nii and
${subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii).
I thought these data would all be in the same atlas space across
subjects, hence I was expecting to find the same vertex coordinates for
all subjects. Instead, when reading the data into matlab (
'ft_cifti_read' and gifti') every subject seems to have their own
distinct vertex locations. Also, the spherical gifti surfaces appear to
be sampled at different coordinates across subjects.
Can I assume that, nonetheless, anatomical correspondence is preserved
across subjects? Could I, for example, take the vertex locations from
${subject}.R.sphere.164k_fs_LR.surf.gii, associate the scalar values in
${subject}.MyelinMap_BC_MSMAll.164k_fs_LR.dscalar.nii to each vertex,
interpolate on the sphere and assume that I can superimpose the results
of this procedure across subjects?
Thanks very much in advance!
Nicola
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